"""
Wrapper over bftools
"""

import os
import subprocess

def convert(input_path, output_path, tile_x=None, tile_y=None, 
            channel=0, series=0, crop_indices = None, bigtiff=False):
    
    """
    Convert an input image in ZEISS LSM or CZI format to an OME TIFF.
    Slice spacing information is lost in this operation for some reason.
    """

    # Set up the command for bfconvert
    bf_tools_dir = os.getenv('BFTOOLS_DIR', os.getcwd()) + "/"
    command = bf_tools_dir + "/bfconvert "
    if not os.path.exists(output_path):
        os.makedirs(output_path)
    output_path += "/" + os.path.splitext(input_path)[0] + "_T%t"
    
    # Only one channel at a time
    command += " -channel " + str(channel) + " "
    output_path += "_C%c"
    # Only one series at a time
    command += " -series " + str(series) + " "
    output_path += "_S%s"

    # Set up tiles
    if tile_x is not None and tile_y is not None:
        command += " -tilex " + str(tile_x) + " -tiley " + str(tile_y) + " "
        output_path += "_tile_X%x_Y%y_ID_%m"
        
    
    # bigtiff
    if bigtiff:
        command += " -bigtiff "
        
    # crop
    if crop_indices is not None:
        command += " -crop " + str(int(crop_indices[4])) + "," + str(int(crop_indices[5])) 
        command += "," + str(int(crop_indices[6]))  + "," + str(int(crop_indices[7])) + " "
        global_index = crop_indices[0] + crop_indices[1]*crop_indices[2]
        output_path += "_x_"+ str(int(crop_indices[0])) + "_y_" + str(int(crop_indices[1])) + "_m_" + str(int(global_index))
    command += input_path + " " + output_path + ".tiff"

    # Do the conversion
    p = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE)
    p.wait()